Organ-specific, blood protein biomarkers for an informative diagnosis of brain and ovarian cancers: technologies for rapid evaluation, validation, and clinical translation Abstract. Our first hypothesis is that organ-specific, secreted biomarkers constitute a molecular fingerprint of the biological networks in each organ. These proteins can change during the progression from health to disease and disease treatment, and provide information relevant to early diagnosis, disease stratification and progression, and therapy response. These markers provide an exciting opportunity for brain and ovarian cancer diagnostics. Our second hypothesis is that highly multiplexed measurements of serum-based protein biomarkers will become a routine clinical tool only if those measurements are quantitative, highly sensitive, and inexpensive. These two hypotheses drive the biology and technology within this project. We describe a blood protein biomarker discovery and validation pathway, as applied to qlioblastoma multiforme (GBM) and ovarian cancer. The pathway begins with the identification of potential organ-specific blood proteins via comparative deep transcriptome analysis, coupled with a search of extant blood protein databases. These biomarkers are pre-validated using unique mass spectrometric methods applied to mouse models and human sera. The most promising markers are translated onto a chip for large scale validation on cancer patients via analysis of a pinprick of blood. The fourth step is to replace the most expensive aspect of those measurements (the antibodies) with a more stable but equal performance alternative. Two nanotechnologies enable this approach. They are protein click-catalyzed capture agents (PCC agents), which are highly modular, chemically synthesized protein capture agents that are assembled by the protein target itself. PCC agents can exhibit the affinity and selectivity of antibodies, but also (bio)chemical and physical stability - thus permitting the routine use of highly multiplexed protein assays. The second nanotechnology permits the routine counting of individual, specific protein molecules, thus extending the sensitivity of multiplexed protein assays by orders of magnitude (and thus to small organs).